bin/config_pipeline.py

   1 #!/usr/bin/python
   2 import subprocess
   3 import re
   4 import logging
   5
   6 logging.basicConfig(level=logging.DEBUG,
   7                     format='%(asctime)s %(levelname)-8s %(message)s',
   8                     datefmt='%a, %d %b %Y %H:%M:%S',
   9                     filename='config_pipeline.log',
  10                     filemode='w')
  11
  12 #Info
  13 s_start = re.compile('Starting Genome Analyzer Pipeline')
  14 s_gerald = re.compile("[\S\s]+--GERALD[\S\s]+--make[\S\s]+")
  15 s_generating = re.compile('Generating journals, Makefiles and parameter files')
  16
  17 #Errors
  18 s_invalid_cmdline = re.compile('Usage:[\S\s]*goat_pipeline.py')
  19
  20 #Ignore
  21 s_skip = re.compile('s_[0-8]_[0-9]+')
  22
  23 def handler(line):
  24
  25   # Irrelevant line
  26   if s_skip.search(line):
  27     pass
  28   elif s_invalid_cmdline.search(line):
  29     logging.error("Invalid commandline options!")
  30   elif s_start.search(line):
  31     logging.info('START: Configuring pipeline')
  32   elif s_gerald.search(line):
  33     logging.info('Running make now')
  34   elif s_generating.search(line):
  35     logging.info('Make files generted')
  36   else:
  37     logging.warning('How to handle: %s' % (line))
  38
  39
  40 def configure():
  41   #ERROR Test:
  42   #pipe = subprocess.Popen(['goat_pipeline.py',
  43   #                         '--GERALD=config32bk.txt',
  44   #                         '--make .',],
  45   #                         #'.'],
  46   #                        stdout=subprocess.PIPE,
  47   #                        stderr=subprocess.PIPE)
  48
  49   #Not a test; actual run attempt.
  50   pipe = subprocess.Popen(['goat_pipeline.py',
  51                            '--GERALD=config32bk.txt',
  52                            '--make',
  53                            '.'],
  54                           stdout=subprocess.PIPE,
  55                           stderr=subprocess.PIPE)
  56
  57   line = pipe.stdout.readline()
  58
  59   while line != '':
  60     handler(line)
  61     line = pipe.stdout.readline()
  62
  63   #print pipe.poll()
  64
  65
  66 if __name__ == '__main__':
  67   configure()